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Due to climate extremes and limited natural resources, especially water, we can expect increased demand in the future for species that can better tolerate climate extremes such as drought. One potentially valuable horticultural species is the endemic species of the Dinaride Mountains Micromeria croatica (Pers.) Schott (family Lamiaceae). It grows in the crevices of carbonate rocks, extending from an altitude of 150 m to more than 2000 m. This study aims to provide additional insight into the genetic and morphological diversity of this endemic species, focusing on valuable horticultural traits. To achieve this goal, morphological and molecular analyses were performed on ten natural populations. Through STRUCTURE and PCoA analyses, ten M. croatica populations were placed into western and eastern genetic groups, with several individuals from western populations assigned to the eastern group and vice versa. These atypical individuals assigned to the new genetic group by BAPS analysis indicate gene flow between western and eastern populations. Similarly, an analysis of molecular variance revealed fewer genetic differences than within studied populations. Both PCA and CANDISC analysis based on eleven morphological traits largely confirmed the existence of two slightly different genetic groups. Two populations containing plants with the most flowers per shoot, one with white-flowered individuals, one with the roundest leaves, and one with the narrowest leaves proved to be the most horticulturally valuable. The genetic and morphological variability found should be a sufficient basis for the potential selection of M. croatica populations and individuals for horticultural purposes. [ABSTRACT FROM AUTHOR]